【Objective】 This study aimed to clarify the relationship between structural characteristic and accumulation of medicinal component in vegetative organs and establish a theoretical foundation for the effective utilization of Mycporum bontioides. 【Method】Plant anatomy and histochemical localization methods were used to study the anatomical structure and accumulation of the main effective components in vegetative organs of M. bontioides. 【Result and conclusion】There were secretory cavities in stems and leaves of M. bontioides, but not in roots. The essential oil was mainly stored in the secretory cavities of stems and leaves, and their surrounding parenchymal cells were involved in the synthesis of essential oil. However, oil was not obvious in roots. The flavonoids were mainly found in the parenchymal cells of roots, stems and leaves. According to their different value, stems and leaves could be used as flavonoids and essential oil extraction for botanical pesticide, while roots, stems and leaves could be used for flavonoids extraction.